--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sort.xml	Sun Dec 22 15:40:15 2024 +0000
@@ -0,0 +1,42 @@
+<tool id="pairtools_sort" name="Pairtools sort" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
+    <description>Sort a 4dn pairs/pairsam file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        pairtools sort
+            '$pairs_path'
+            -o '$output_sorted_pairs'
+            --nproc-in \${GALAXY_SLOTS:-4}
+            --nproc-out \${GALAXY_SLOTS:-4}
+    ]]></command>
+    <inputs>      
+        <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input file" help="Input a 4dn pairs or pairsam file"/>
+    </inputs>
+    <outputs>
+        <data name="output_sorted_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}">
+        </data>
+    </outputs>
+    <tests>
+        <!--Test default parameters with pairs file-->
+        <test expect_num_outputs="1">
+            <param name="pairs_path" value="output_parsed_pairs_bam.pairs"/>
+            <output name="output_sorted_pairs" file="output_sorted_pairs.pairs" lines_diff="10"/>
+        </test>
+        <!--Test default parameters with pairsam file-->
+        <test expect_num_outputs="1">
+            <param name="pairs_path" value="output_dedup_pairs_markdups.pairsam"/>
+            <output name="output_sorted_pairs" file="output_dedup_sorted.pairsam" lines_diff="10"/>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+        **Pairtools sort**
+
+        Sort pairs in the lexicographic order along chrom1 and chrom2, in the numeric order along pos1 and pos2 and in the lexicographic order along pair_type.
+        
+    ]]></help>
+    <expand macro="citations"/>
+    <expand macro="creator"/>
+</tool>